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Curoverse Internship

Recently I started work at Curoverse, which I like to describe as “the cloud for genomes,” and I like to describe my job as “being paid to work on open-source bioinformatics software.”

I think the official site has some more informative words to say on this subject and talks about the vision of enabling biomedical information sharing to improve research and clinical outcomes or something.  Anyway, I’m an intern so thankfully I haven’t had to pitch the idea repeatedly every day until I can present it in a concise and powerful manner 🙂

I’ve been having a great time. I mean, it’s (a) open-source (b) bioinformatics (c) python (d) has nothing at all to do with cruel cruel robots.  😛

I’ve learned a lot about genomes, sequencing, and all the pitfalls of genomes, aka why Arvados (the open-source platform Curoverse is working on) is needed:


That is fifty phased genomes, shipped on multi-terabyte hard drives to us. Sneakermaillll!

Here are some important things I have learned during the month or so I’ve been at the job so far:

1) Our mascot is called Dax. It is adorableeeeee


No, we don’t have plushies of Dax yet, but soon!

Oh! I could easily revolve this and make a 3d model that I could print off this weekend. Hmm. *adds to todo list*

2) In software, open-source is much more established and can be seen as a boon by customers, especially by researchers and clinical or governmental infrastructure.

3) Having a stable source of income is great! Having really knowledgeable co-workers is great! Having an office with an ergonomic chair and free tea is great! Plus, all my work is open-source, so I can easily refer to it in the future, or point people / my friends at it.

4) It’s been super interesting to see the sales and development cycle. I’ve been observing Curoverse’s strategies for finding the so-called “product-market fit” and the continual effort to find and work on what customers want — in some senses, selling something before developing it.

Okay, I’m sort of just rambling here, so I’ll talk a little bit about the environment I’ve found myself in and the work I’ve been doing.

1) Environment:

The location is great. It’s a few minutes walk from the South Station stop on the Red Line, and within walking distance to Chinatown as well as views of the water.


It’s all open-style desks, no cubicles. Everyone’s right next to each other, and furthermore EVERYONE IS ON IRC. (even some of our customers apparently!). It works surprisingly well, since I’ve had cases where I’ll ask someone a question (in the team chat) and someone else will give me a faster way to do it / enable me to do it myself. It’s still not zephyr with its classes that let you sort through a multi-threaded conversation easily, but it’s nice.

Unlike what I’ve come to expect of software development, a lot of the folks are older / married / have kids, and also have more engineering experience of course. There’s also a GPL ninja floating around…

What really puzzled me at first was calling one section of software developers “engineering” and another “science,” but it makes sense now. I just expected the engineering team to be building more robots I guess. ^^;

The engineering team operates on “agile” development (or lean?) — anyway the main thing to me is they are always talking about stories, which amuses me. I imagine them typing away drafting a really epic novel sometimes.

The science team, which I have found myself on, has standups every day as well, were we all stand up and present to the rest of the team what we’ve been up to.  Standing up hasn’t seemed very effective at keeping our standup short though o_o

Every Friday there is also free lunch err I mean, a company meeting, which keeps everyone on the same page.

Oh! I got to attend the first Curoverse social.


Delicious pizza (flatbread) and bowling! It was candlepin bowling, where the pins are flattened like candlesticks instead of like the traditional bowling pin and the balls are solid and a bit bigger than a softball.


(yep, people are wearing their work outfits, which vary a lot).

2) What I’ve been working on.

Right away I got involved in working with GA4GH, aka the Global Alliance for Genomics and Health, or more accurately working on projects the GA4GH groups determine are important. I made a little python+flask webapp and learned how to serve it using uWSGI and nginx,as well as learned a bit of working with postgresql (such as the fact that DISTINCTs take a significant chunk of time, aka seconds, because they query across the whole table!).

Screenshot from 2014-10-16 15:04:30

I’ve also been playing around with javascript to make POSTs to an API and return the results.

Screenshot from 2014-10-16 15:04:26

OH! AND WRITING TERRIBLE BASH SCRIPTS because apparently bioinformaticians not only can’t agree on whether to 0-index or 1-index, but also make these convoluted file formats followed by convoluted file-format-conversion tools that require specifically named files in certain directories all documented in a PDF somewhere on the internet. WHYYYY

Screenshot from 2014-10-16 15:08:26

Hmm, well, now I feel like I haven’t done much since I can sum it all up in three images. Regardless, I sure have learned a lot while getting paid to do so, and I’ve always had plenty of work to do. There’s in fact a GA4GH conference this weekend where my supervisor might demo some of my work as part of the science team’s work, which is nifty.

See you all next time!

todo list 9/9/14

hello there friends!

just a casual post here. this is on my todo list:


  • finish virginia backpacking trip post
  • finish fairhaven -> boston bluewater sailing post
  • thoughts on kickstarter and startups


  • r/ga
  • YC
    • find alums who have done YC
    • make statistical gif cakes
    • finish application
  • tech stars
  • lemnos labs
  • bolt


  • DFM
  • that long post -about casting
  • e4c discussions
  • education terminology
  • friends’ blogs!


  • spanish
  • sailing
  • D3
  • javascript visualizations
  • ML things
  • database architecture
  • android
  • ruby on rails
  • CTF stuff
  • openCV
  • get better at git

classes to finish

  • 6.004, 6.302, 6.003, 6.033, 6.046, 6.006, 6.034
  • http://web.mit.edu/catalog/degre.engin.ch6.html
  • quadcopter class
  • 18.06
  • some statistics class or other


  • ukulele book
  • outboard motor


  • android / openCV resistor value recognition
  • resume (update), portfolio website (organize blog)
  • flash laptop bios


  • accounting/taxes
  • payroll
  • app inventor ble block
  • 6.01 robot cost reduction / robustness
  • gatttool 5 unit block

26 foot 1967 Boat: Massive Update pt1


A few months ago Cappie (co-founder of NarwhalEdu) and I bought a boat off  craigslist for a very small amount of money and have since been working on attaching pieces and getting her shipshape again.

We actually could have gotten her in the water much sooner if it weren’t for several mishaps with the registration and titling office until finally we got on the phone with the right person.

Here’s a summary of our trials and tribulations with the boat. I’ve been keeping it under wraps (har har… it has actually been under a tarp for weeks now), but over the last few months have gently broken the news to my parents that I will be living on this boat. So now I’m free to blog about it!

First Impressions


Cappie found the boat on craiglist in February while looking for a dinghy. It was listed for $500. Wow! What was up with that — a 26 foot boat for that much? Was it falling into pieces? After some conversations back and forth that went roughly like this:

Cappie: So, how do you feel about twenty-six foot boat.

Nancy: Lol wat? …seems lulzy.

Nancy: …wait, are we actually serious about this?

Cappie: I dunno.

Nancy: … … I dunno either. Lol! Boat!

Cappie: Boat!

we decided to investigate right away. We weren’t sure why someone would sell it for this price. Cappie theorized that maybe some older guy just wanted the boat to be in good hands with some youngsters. I was very skeptical of this, but it turned out to be the case!

We got some input from our friends who said things like:

“Boat stands for Bring Out Another Thousand” and “The happiest days of a boat owner’s life are the day she buys the boat and the day she sells it.” One person said simply “Don’t do it” and refused to talk to us further. Well. One thing everyone agreed on was that the woodwork inside was beautiful. The owner at the time was a carpenter and had spent many years working on this boat.

After some consideration we decided to go for it. The money would only be $100 up-front and we could at any stage decide to abandon the project.

Initial Work

  1. Lightly sanded the whole keel while wearing respirators. Lead paint yay! Orbital sanders were used
  2. Lightly sanded the deck down to prepare for a new deck paint job. Sandpaper was used
  3. Removed a lot of junk from inside the boat and vacuumed the whole place.
  4. Scrubbed mildew off the roof and other places

On the bureaucracy side, mostly we just got really angry and frustrated because it sounded like they wanted us to pay 20 years of excise taxes on a boat that was never used. As recent college graduates working on startup, a few hundred dollars is a significant chunk of change.


At that point, we needed to move the boat out of the Worcester warehouse it was stored in since the warehouse was scheduled to be torn down.

We asked around and finally learned that marinas in Boston all wanted insurance, which we couldn’t get without a hull ID number, which we didn’t have because our boat was so old. However, we found a marina that was kind enough to put us up. We found them through a trailering service they advertised on their website. Turns out, they drove all the way down only to learn that their trailer was too big to fit inside the warehouse between the warehouse pillars!


Sad. But they were able to recommend to us someone else who had a smaller trailer.  And man, seeing the hydraulic lifters in action was pretty sweet (the big trailer even had wireless controls for one), as well as just how awesome the drivers were at driving geometry and precise maneuvers, and seeing the drivers confidently pull out the stands and “jenga” out the blocks was impressive.


Well, $500 later (and a bunch of effort securing the mast down and bringing it on top of the boat) the boat was in Fairhaven. We wrapped it up in a tarp and left it there.

A few weeks later, we return to find a flood inside… we hadn’t noticed because after it rained it would dry out and drip out over a few days. The beautiful woodwork warped even. We puzzled over what was going on and where the water was coming from for a while, before realizing that there were several holes we didn’t tape over in the bow and also


there was a valve that we hadn’t opened to let all the rainwater coming in through the deck drains out. DERP. It actually poured out water for several minutes like that and formed a small lake.

Next update: Janky watt-hour testers for boat batteries, honeycomb nest discovery, HIN dremeling, EPO inspection and detective work (what is the boat actually?), registration and titling issues, troubleshooting an old outboard motor, and attaching the gunnels and trim, costs of living in a marina (liveaboard) vs paying rent.